When Malcolm Smith became Senate majority leader last January, he rewarded longtime associate Joan Flowers — his former campaign treasurer and the lawyer for a politically connected charity now under federal probe — with a $145,396-a-year, full-time Senate job.

She had previously done temporary stints for the Senate during legislative sessions from 2002 to 2007, when Gov. Paterson was Senate minority leader.

Flowers, a Queens Democratic operative, also worked as campaign treasurer for Paterson and Rep. Gregory Meeks.

Flowers raked in $249,727 from 2000 through 2009 from the Smith and Paterson campaigns and Smith’s political action committee, state records show. The money went both to her and to her company, Jaymacdee Consultants, and includes reimbursements for wages and professional and consulting services.

Flowers was Meeks’ campaign treasurer during a period when the Federal Elections Commission found he used campaign contributions to hire a personal trainer and for the lease and repairs of a car. Meeks was hit with $63,000 in civil penalties in 2008.

For years, Flowers, 62, had a law office in a one-story building on South Conduit Avenue in Springfield Gardens, where a billboard still advertises her legal services. Her husband, Neville, has a physical-therapy practice there.

The building also served as the address for the New Direction Local Development Corp. for most of its existence. The charity is now being eyed by investigators.

Federal tax forms show that the nonprofit’s books were held specifically in Flowers’ office in 2002, 2004 and 2005.

Flowers’ son, Michael, was on New Direction’s founding board of directors, along with Smith’s wife. In 2000, Joan Flowers drew up the incorporation papers for the nonprofit, which was founded with help from Smith and Meeks.

Federal investigators are looking at New Direction after The Post reported last month that it took in hundreds of thousands of dollars, including taxpayer funds, with little accountability for how it spent the money. Its fund to help Katrina victims took in at least $31,000 but donated only $1,392 to help families, a Post review of tax records found.

Smith and Meeks have disavowed any association with New Direction’s day-to-day operations.

Smith, Meeks and Flowers also worked together on another nonprofit together, the Merrick Academy charter school in Queens, where they were board members.